[phenixbb] data fill in in phenix refine?

Ursula Schulze-Gahmen uschulze-gahmen at lbl.gov
Fri Oct 13 11:47:57 PDT 2017

I have data from a crystal with anisotropic diffraction. After scaling and
merging using the webserver staraniso, I would like to refine using phenix
refine. Could you tell me if phenixrefine will try to fill in the missing
reflections that were removed in the staraniso procedure? If so, is there a
a way to prevent this fill in? Following is the warning message for the
Staraniso server:

We are grateful to Andrew Leslie (MRC-LMB) for identifying a potentially
undesirable 'feature' of CCP4/REFMAC (and possibly other refinement
software), namely the 'fill-in' of unobserved data with *DF*calc which
makes it effectively *incompatible* with the MTZ file output by STARANISO.
Our advice is therefore to use *BUSTER
<http://www.globalphasing.com/buster>* for refinement using the downloaded
MTZ file, unless the user can find a way to disable that feature in the
alternative software.

In general, any treatment of STARANISO's output data that adds missing
reflections out to the resolution limit may result in a very high
proportion of unobserved data compared with data that have had a cut-off
applied according to an isotropic criterion.  Where missing reflections
have been added in this way the user should take care to verify that any
applications used to process the data subsequently can handle it correctly.


Ursula Schulze-Gahmen, Ph.D.
Project Scientist
UC Berkeley, QB3
360 Stanley Hall #3220
Berkeley, CA 94720-3220
(510) 643 9491
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